mutation-driven evolution.pdf

mutation-driven evolution.pdf

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Mutation-DrivenEvolutionMasatoshiNeiPennsylvaniaStateUniversity1Mutation-DrivenEvalution.FirstEdition.MasatoshiNei.MasatoshiNei2013.Published2013byOxfordUniversityPress.3GreatClarendonStreet,Oxford,OX26DP,UnitedKingdomOxfordUniversityPressisadepartmentoftheUniversityofOxford.ItfurtherstheUniversitysobjectiveofexcellenceinresearch,scholarship,andeducationbypublishingworldwide.OxfordisaregisteredtrademarkofOxfordUniversityPressintheUKandincertainothercountriesMasatoshiNei2013ThemoralrightsoftheauthorhavebeenassertedFirstpublished2013Impression:

1Allrightsreserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmitted,inanyformorbyanymeans,withoutthepriorpermissioninwritingofOxfordUniversityPress,orasexpresslypermittedbylaw,bylicenceorundertermsagreedwiththeappropriatereprographicsrightsorganization.EnquiriesconcerningreproductionoutsidethescopeoftheaboveshouldbesenttotheRightsDepartment,OxfordUniversityPress,attheaddressaboveYoumustnotcirculatethisworkinanyotherformandyoumustimposethissameconditiononanyacquirerBritishLibraryCataloguinginPublicationDataDataavailableISBN9780199661732PrintedandboundbyCPIGroup（UK）Ltd,Croydon,CR04YYLinkstothirdpartywebsitesareprovidedbyOxfordingoodfaithandforinformationonly.Oxforddisclaimsanyresponsibilityforthematerialscontainedinanythirdpartywebsitereferencedinthiswork.ContentsPrefaceix1SelectionismandMutationism11.1DarwinsTheoryofEvolution11.2CriticismsofDarwinsTheory21.3EvolutionbyDiscontinuousVariation31.4Mutationism61.5Neo-Darwinism71.6NeomutationismorMutation-DrivenEvolution91.7SurvivaloftheFittestandSurvivaloftheNiche-FillingVariants92Neo-DarwinismandPanselectionism132.1Backgrounds132.2AlleleFrequencyChangesastheBasicProcessofEvolution14Mutation14NaturalSelectionwithConstantFitness15Mutation-SelectionBalance17BalancedPolymorphism18NaturalSelectionforMultipleLoci192.3DifficultiesofDefiningandEstimatingSelectionCoefficients20EstimatesofSelectionCoefficientsandtheirReliability20FluctuationofSelectionCoefficients22GeneralConsiderations232.4StochasticChangesofAlleleFrequencies24ProbabilityofFixationofMutantAlleles25EquilibriumDistributionofAlleleFrequencies25EffectivePopulationSizeandSamplingErrorsofAlleleFrequencies28RandomErrorsCausedbyFluctuationofSelectionCoefficients292.5MutationandStandingGeneticVariation31ArtificialandNaturalSelectioninQuantitativeCharacters31EvolutionofDrugResistance342.6ClassicalandBalanceTheoriesofMaintenanceofGeneticVariation34GeneticLoad35NumberofAllelesthatcanbeMaintainedinFinitePopulations362.7NaturalSelectionasaCreativeForce372.8Summary39iiiivCONTENTS3EvolutionaryTheoriesintheNeo-DarwinianEra413.1ModifierGenes41EvolutionofDominance42ModificationofLinkageIntensity433.2FishersFundamentalTheoremofNaturalSelection443.3CostofNaturalSelectionandFertilityExcessRequired463.4ShiftingBalanceTheoryofEvolution483.5AccumulationofNonfunctionalandDeleteriousMutations50YChromosomes50NonfunctionalMutationsinDuplicateGenes52DeleteriousMutationsandMullersRatchet523.6BottleneckEffectsandGeneticVariability533.7BeanbagGeneticsandEvolution563.8Summary584MolecularEvolution594.1EarlyStudiesofMolecularEvolution594.2NeutralEvolutionattheProteinLevel60CostofNaturalSelectionandNeutralTheory60DefinitionofNeutralMutations61KingandJukessView63DefinitionofNeutralTheory644.3MolecularClocks65EvolutionaryRateunderPurifyingSelection65EvolutionaryRateandGenerationTime65FunctionalConstraintsofProteins66VariationinMutationRate67MolecularClocksandNeutralTheory684.4EvolutionofProtein-CodingGenes69GeneralPropertiesofEvolutionofProtein-CodingGenes69Fast-EvolvingGenes704.5ProteinPolymorphism704.6NeutralEvolutionattheDNALevel72SynonymousandNonsynonymousNucleotideSubstitutions72PseudogenesasaParadigmofNeutralEvolution72SlightlyDeleteriousorNearlyNeutralMutations734.7AdvantageousMutations74EvolutionofNewProteinFunction74ImmuneSystemGenes78Trans-SpeciesPolymorphism794.8RecentStatisticalStudiesforDetectingPositiveSelection81BayesianMethodsforIdentifyingPositively-SelectedCodonSites81MKTestanditsExtensions82ExtendedHaplotypeHomozygosityandFSTTests84StatisticalStudiesandBiochemicalVerification86FrequencyDistributionsofMutantNucleotides874.9Summary87CONTENTSv5GeneDuplication,MultigeneFamilies,andRepetitiveDNASequences895.1NewGenesGeneratedbyGeneDuplication89IncreaseintheNumberofGenesbyGeneDuplication90GenomeSizeandNumberofGenes91GeneNumbersandPhenotypicComplexity925.2EvolutionofMultigeneFamilies945.3ConcertedEvolution95UnequalCrossover,GeneConversion,andPurifyingSelection95TandemlyArrayedHistoneGenes965.4Birth-and-DeathEvolution97MHCGenes97ImmunoglobulinsandotherImmuneSystemsGenes99OlfactoryandotherChemosensoryReceptorGenes101Birth-and-DeathEvolutionwithStrongPurifyingSelection1025.5MultigeneFamiliesandEvolutionofNewGeneticSystems103AdaptiveImmuneSystem103HomeoboxGenesInvolvedinAnimalandPlantDevelopment104MultigeneFamiliesandFlowerDevelopmentinPlants1055.6GenomicDriftandCopyNumberVariation1055.7NoncodingDNAandTransposableGeneticElements107ExonsandIntrons108TransposableGeneticElements109TandemRepetitiveSequences1105.8Summary1106EvolutionofPhenotypicCharacters1136.1ChangingConceptsoftheGeneandGeneExpression113DefinitionofaGene113Protein-CodingandRegulatoryRegionsofGenes115GeneRegulatoryNetworks116SmallRNAsthatControltheLevelofGeneExpression116MethylationandEpigenetics117SignalingPathwaysandGeneInteraction1186.2EvolutionofPhysiologicalandMorphologicalCharacters120ChangesintheProtein-CodingRegionsofGenes120GeneRegulationHypothesis122MajorGeneEffectHypothesis126GeneRegulatoryNetworksandMorphologicalEvolution1286.3EvolutionofGeneRegulatorySystems129Cis-RegulatoryElements129EvolutionaryChangeofMicroRNAsandotherSmallRNAsControllingGeneExpression1306.4EpigeneticsandPhenotypicEvolution131EnvironmentalSexDetermination131EvolutionofTemperature-DependentSexDetermination132VernalizationandFloweringinPlants132viCONTENTS6.5GeneCo-OptionandHorizontalGeneTransfer133GeneCo-Option133HorizontalGeneTransfer134PhotosyntheticAnimals1356.6Summary1367MutationandSelectioninSpeciation1377.1SpeciationbyChromosomalMutations138FormationofNewSpeciesbyPolyploidization138ChangesofGenomicStructuresandSpeciation139ChromosomalRearrangementsandSpeciation1407.2EvolutionofReproductiveIsolationbyGenicMutation141OkaModelofSpeciationbyDuplicateGeneMutations141Dobzhansky-Muller（DM）ModelofEvolutionofReproductiveIsolation143MultiallelicComplementaryGenesModel146Single-LocusSpeciation1487.3ReproductiveIsolationbyComplexGeneticSystems149SegregationDistortersandSpeciation149Heterochromatin-AssociatedHybridIncapacity1507.4OtherMechanismsofEvolutionofReproductiveIsolation1507.5SpeciationbyBottleneckEffects1517.6HybridSterilityGeneratedbyPassiveProcessofPhenotypicEvolution1527.7Summary1538AdaptationandEvolution1558.1AdaptationbyMutation1558.2EvolutionofSomeSpecificCharacters156EvolutionofEyesandPhotoreceptors156EvolutionofCasteSystemsinHoneybeesandsomeotherInsects157EvolutionofAsymmetricMorphologyinFlatfish,Snails,andotherOrganisms1618.3RegressiveEvolutionandPseudogenes162UniversalityofVestigialCharacters162MolecularBasisofRegressiveEvolution162ParasiticOrganismsandtheirGenomicChanges1658.4EvolutionofSex-DeterminationMechanisms166SexDeterminationinVertebrates167SexDeterminationinInvertebrates1698.5DegenerationoftheY（W）Chromosome171YDegenerationandDosageCompensation171MolecularBasisofX-ChromosomeDosageCompensation172EvolutionbySexuallyAntagonisticMutations1738.6EvolutionofBehavioralCharacters174SelfishGeneTheoryofEvolution174MolecularStudiesofBehavioralGenes1758.7Summary177CONTENTSvii9MutationandSelectioninEvolution1799.1DistinctProcessesofMutationandSelection1799.2RandomFactorsandGeneCo-OptioninEvolution1819.3RetrospectiveandProspectiveStudiesofEvolution1829.4GenomicConstraintsandConstraint-BreakingEvolution183ProgressiveEvolution183OriginofLifeWithoutPurpose183Constraint-BreakingEvolution1849.5GeneticVariationwithinSpecies1859.6Niche-FillingEvolution18610GeneralSummaryandConclusion189Appendix:

MathematicalNotes201A.AlleleFrequencyChangesDuetoNaturalSelection201DeterministicModelsforAlleleFrequencyChanges201EquilibriumFrequenciesDuetoMutationandSelection201B.AlleleFrequencyDistributionsundertheInfinite-SiteModel202C.TemporalFluctuationofSelectionCoefficients202GeneralComments202D.ArtificialSelectionforQuantitativeCharacters203E.GeneticLoad203MutationLoad204SegregationLoad204F.BayesianMethodofDetectingPositivelySelectedCodons204References207AuthorIndex233SubjectIndex238ThispageintentionallyleftblankIstartedmycareerwiththeoreticalpopulationgeneticsinthe1960safterashortperiodoffieldworkexperienceconcerningquantitativegenetics.Atthattimeevolutionar